Fix flamingpy build and CI (#127)

* add panda to dev requirements

* fix some tests

* run black

* backwards-compatible sparse check

* fix missed test and RTD

* changelog

* add name to contribution

* undo xfail

.github/CHANGELOG.md

@@ -8,6 +8,7 @@
 * An instance of a depracated `fig.gca` with a keyword argument was fixed. [#124](https://github.com/XanaduAI/flamingpy/pull/124)
 * Remove the tight layout setting from `draw_EGraph_matplotlib`, which was causing a warning. [#125](https://github.com/XanaduAI/flamingpy/pull/125)
 * Bump tj-actions/branch-names from 5 to 8 to fix vulnerability. [#126](https://github.com/XanaduAI/flamingpy/pull/126)
+* Apply minor tweaks to source code and tests to update compatibility across Python versions. [#127](https://github.com/XanaduAI/flamingpy/pull/127)
 
 ### Improvements
 
@@ -21,7 +22,7 @@
 
 This release contains contributions from (in alphabetical order):
 
-Nariman Saadatmand
+Nariman Saadatmand, [Matthew Silverman](https://github.com/timmysilv)
 
 See full commit details ...
 

.readthedocs.yml

@@ -19,4 +19,3 @@ python:
       - requirements: doc/dev_requirements.txt
       - method: setuptools
         path: .
-    system_packages: true

dev_requirements.txt

@@ -15,3 +15,4 @@ scipy>=1.6
 thewalrus>=0.19.0
 plotly>=4.5.0
 pylint==2.13.5
+pandas>=2.0

doc/tutorials/run_error_correction.py

@@ -4,7 +4,6 @@
 ====================================
 """
 
-
 ######################################################################
 # *Author: Ilan Tzitrin*
 #

doc/tutorials/run_graph_states.py

@@ -4,7 +4,6 @@
 ============
 """
 
-
 ######################################################################
 # *Authors: Ilan Tzitrin and Luis Mantilla*
 #

flamingpy/cv/ops.py

@@ -28,6 +28,11 @@ def invert_permutation(p):
     return p_inverted
 
 
+def issparse(array):
+    """Check if an array is sparse. Backwards-compatible with old SciPy versions."""
+    return isinstance(array, getattr(sp, "sparray", sp.coo_matrix))
+
+
 def SCZ_mat(adj, sparse=True):
     """Return a symplectic matrix corresponding to CZ gate application.
 
@@ -59,7 +64,7 @@ def SCZ_mat(adj, sparse=True):
     # Construct symplectic
     symplectic = block_func([[identity, zeros], [adj, identity]])
 
-    if not sparse and isinstance(symplectic, sp.coo_matrix):
+    if not sparse and issparse(symplectic):
         return symplectic.toarray()
 
     return symplectic

flamingpy/decoders/unionfind/algos.py

@@ -108,19 +108,21 @@ def initialize_cluster_trees(stabilizer_graph):
         root_stabilizer = erasure_graph_nodes[component.pop()]
         cluster_root = Root(
             node_dict[root_stabilizer],
-            parity=root_stabilizer.parity
-            if isinstance(root_stabilizer, Stabilizer)
-            else "boundary",
+            parity=(
+                root_stabilizer.parity if isinstance(root_stabilizer, Stabilizer) else "boundary"
+            ),
         )  # boundary nodes are represented by tuples
         for vertex in component:
             vertex_stabilizer = erasure_graph_nodes[vertex]
             union(
                 cluster_root,
                 Root(
                     node_dict[vertex_stabilizer],
-                    parity=vertex_stabilizer.parity
-                    if isinstance(vertex_stabilizer, Stabilizer)
-                    else "boundary",
+                    parity=(
+                        vertex_stabilizer.parity
+                        if isinstance(vertex_stabilizer, Stabilizer)
+                        else "boundary"
+                    ),
                 ),
             )
         if cluster_root.parity:

flamingpy/examples/lc_equivalence.py

@@ -1,4 +1,5 @@
 """Example for testing LC equivalence of graph states."""
+
 from flamingpy.utils.graph_states import star_graph, complete_graph, linear_cluster, ring_graph
 
 print("Testing LC equivalence of graph states:", "\n")

flamingpy/simulations.py

@@ -30,7 +30,7 @@
 try:
     import mpi4py.rc
 
-    mpi4py.rc.threaded = False
+    mpi4py.rc.threads = False
     from mpi4py import MPI
 except ImportError:  # pragma: no cover
     warnings.warn("Failed to import mpi4py libraries.", ImportWarning)

tests/cv/test_cv_ops.py

@@ -25,7 +25,7 @@
 import scipy.sparse as sp
 
 from flamingpy.codes.graphs import EGraph
-from flamingpy.cv.ops import invert_permutation, SCZ_mat, SCZ_apply
+from flamingpy.cv.ops import invert_permutation, SCZ_mat, SCZ_apply, issparse
 
 now = datetime.now()
 int_time = int(str(now.year) + str(now.month) + str(now.day) + str(now.hour) + str(now.minute))
@@ -50,13 +50,11 @@ def random_graph(request):
 class TestSCZ:
     """Tests for symplectic CZ matrices."""
 
-    @pytest.mark.parametrize(
-        "sparse, expected_out_type", sorted([(True, sp.coo_matrix), (False, np.ndarray)])
-    )
-    def test_SCZ_mat_sparse_param(self, random_graph, sparse, expected_out_type):
+    @pytest.mark.parametrize("sparse", [True, False])
+    def test_SCZ_mat_sparse_param(self, random_graph, sparse):
         """Tests the SCZ_mat function outputs sparse or dense arrays."""
         SCZ = SCZ_mat(random_graph[2], sparse=sparse)
-        assert isinstance(SCZ, expected_out_type)
+        assert issparse(SCZ) if sparse else isinstance(SCZ, np.ndarray)
 
     def test_SCZ_mat(self, random_graph):
         """Tests the SCZ_mat function."""
@@ -65,7 +63,7 @@ def test_SCZ_mat(self, random_graph):
         # Check if SCZ_mat adjusts type of output matrix based on
         # type of input.
         assert isinstance(SCZ, np.ndarray)
-        assert isinstance(SCZ_sparse, sp.coo_matrix)
+        assert issparse(SCZ_sparse)
         # Check that structure of SCZ matrix is correct.
         for mat in (SCZ, SCZ_sparse.toarray()):
             assert np.array_equal(mat[:N, :N], np.identity(N))

tests/examples/test_examples.py

@@ -17,6 +17,7 @@
 # pylint: disable=import-outside-toplevel,unused-import
 
 import pytest
+import numpy as np
 from flamingpy.codes import alternating_polarity
 
 
@@ -31,7 +32,7 @@ def test_decoder_example(noise, decoder):
     ec = "primal"
 
     result = decode_surface_code(distance, boundaries, ec, noise, decoder, draw=True)
-    assert result.__class__.__name__ == "bool_"
+    assert isinstance(result, np.bool_)
 
 
 def test_gkp_example():